POPULATION BIOLOGY
BEHAVIORAL ECOLOGY
&
We are so glad you stopped by our blog! We plan to post here often to keep you updated on all the exciting things happening for PBBE. You will get a glimpse into what daily life looks like for research scientists, lab technicians and a volunteer. This is an informal place for us to keep you current and show you a bit of our personalities (we are really funny, we swear!).
Some days are more interesting than others (which we will probably post about), and some days break throughs are made (usually Friday's, after 5pm). Science is hard work. Getting funding for science is even harder work. Thankfully, we work with some awesome people, which make the long days more bearable. Check back with us often, and hopefully you enjoy reading about all the fun we have while working!
Welcome to the PBBE blog!
March 6, 2014
Most recent posts:
Family Reunion: Beluga Edition
April 6, 2018
Our publication in PlosONE caught a bit of international attention this week. Read about how our large scale population genetics study demonstrates that beluga whales are sharing their knowledge with close kin and offspring, and making a case for cultural inheritance.
Here are a few of the press releases about the paper:
http://www.newsweek.com/beluga-whales-value-culture-and-ancestral-roots-much-humans-873878
https://www.sciencedaily.com/releases/2018/04/180405093217.htm
https://www.earth.com/news/beluga-whales-prioritize-family/
A Stellar Presentation
February 14, 2018
Greg enlightened the Ocean Science Lecture Series audience about The Saga of Stellar's sea lion in the Aleutian Islands. True to his Irish roots, famed for their oral tradition, Greg wove a tale bursting with history, danger, hilarious anecdotes, science and videos that kept the auditorium captivated 'til the very end.
Also, check out some of his awesome fieldwork footage!
Tissue Extractions
February 2018
We have some exciting things happening in the lab next week. So to prepare, we did some fresh extractions of frozen muscle.
Check out what two days of work looks like in 45 seconds. Happy Friday ya'll!
2018
January 2018
Happy New Year! We hit the ground running with a new publication; download it from our publications page as soon as it's available, and read the press release summary here:
DNA ‘fingerprinting’ helps monitor whale numbers in Alaska
Harbor Branch Oceanographic Institute’s Population Biology and Behavioral Ecology Program are using DNA ‘fingerprinting’ to monitor the population size of beluga whales in Alaska. Collaborating with Alaska Natives and with scientists from the Alaska Department of Fish and Game and the National Marine Fisheries Service, the FAU team of Greg O’Corry-Crowe, Tatiana Ferrer and Brooke Potgieter co-authored a paper that came out today in the journal Marine Mammal Science. The small population of beluga whales in Bristol Bay, Alaska has received increasing attention in recent years over concerns about the potential impacts of climate change, oil and gas development and mining within the headwaters of Bristol Bay rivers, home to the largest commercial sockeye salmon fishery in the world. Efficient, reliable estimates of abundance and trend are critical to effective management of this population. However, almost every aspect of studying marine mammals, especially in the seasonally ice covered waters of the North, is challenging. Estimating abundance and monitoring trends in beluga whales has relied on aerial surveys which are both costly and prone to many sources of bias. The team, therefore, took a radically different approach: Genetic Mark-Recapture. This approach adapts the principals of mark-recapture abundance estimation by using DNA profiling of individual whales to detect genetic ‘recaptures’ from subsequent sampling efforts. By systematically collecting tiny tissue biopsies from free-swimming whales over several years and conducting the DNA ‘fingerprinting' at the HBOI lab, the team was able to estimate the size of the population from the frequency of ‘recaptured’ (i.e. re-sampled) individuals in their sample set. The study has established the method as an effective alternative approach to population monitoring of beluga whales worldwide and of other cetacean species.
Bye 2017
December 2017
Bye 2017
December 2017
Don't let the door hit you on the way out!
Like for most of us, 2017 was a rough year. We said goodbye to it over a holiday lunch at Ocean Grill on the beach (pre bomb cyclone, so weather was lovely and warm)! Laura is moving on and won't be part of PBBE in 2018. Don't worry, she's not going far! We wish her the best of luck in her new bioinformatics position with Dr. Dickens at HBOI!
PBBE goes to Canada, eh!
October 2017
Four of us presented at the Biennial Conference this year, which was in beautiful Halifax, Nova Scotia. We caught up with several colleagues, made many more contacts, and engaged with researchers from around the world.
In addition to learning about the latest scientific research being conducted on marine mammals right now, we also provided a tour de force of genetics; informing and educating scientists about the breakthroughs our lab is making in the world of immune function genes on non model organisms and their role in the health and adaptability of an individual and, ultimately, a population.
To see our posters and other published research, see the publications page. (Check back frequently, as we have many papers in prep and being published currently!)
Summer Field Log: part 2
Summer 2017
Week 2:
"Arrived in Adak, the central Aleutians, June 22 to board the Tiglax for a Steller sea lion research cruise run by NOAA Fisheries. We set out in a squally night and headed west all the way to Attu Island, the western most Island in the chain. We stopped along the way to do some brand-resight work and to do some maintenance of stationary cameras at sea lion rookeries on Buldir and Alaid islands. We rounded Cape Wrangell on Attu's west side, the western-most point in the Americas on June 25th. Then on to Agattu where we did some more re sight work, hexacopter surveys and pup catching for marking and sampling work. Moving further east to Kiska and then Ulak we spent a few days waiting for the right conditions to land a shore crew to catch, mark and sample pups. We were greeted one morning by the sight of 2 killer whales working the shoreline right off the rookery. So close they sometimes partially beached on the slanted rock slab the Stellers had hauled out on. What an epic day observing killer whales move in on one Steller group after another. Regularly, the larger bulls and some of the other adults would dive into the water, followed by encounters with the whales only to have the sea lions leap out on shore once more. All this going on while we're perched on a knife-edge ridge doing maintenance on cameras. Surreal. The following day saw another larger group of killer whales appear. More business-like, this group were more focused and efficient when it came to hunting sea lions. We successfully sampled another 50 pups on the Ulak rookery during the catching and marking operations for our genetic research. Add to all this incredible bird life, wild seascapes and stunning scenery in one of the most remotest parts of the world and you get the experience of a lifetime."
R/V Tiglax
Summer 2017
Ever wonder what life looks like on a research vessel? This video shows the ins and outs of Greg's "home away from home" while cruising around the Aleutians this summer.
Land of the Midnight Sun
Summer 2017
Like the snowbirds, we fly north for the summer. Greg is conducting fieldwork in Alaska and is periodically checking back in with updates. Here is his account from the first week:
"Well, week one of this summer’s Alaska trip is over and here are some of the highlights. I made it in to Barrow in the evening of June 13th, nearly 20 hours from when I awoke in the wee hours in Florida. I was glad to see that my favorite spot out at the Arctic Research Facility (ARF), a tiny cabin affectionately known as the ‘Fortress of Solitude’, was available. At barely seven foot square there’s just about enough room for a bunk and a small chest of drawers. But it’s cozy once the heater has been on for 30min or so. So this was to be my domicile for the next 5 nights. The snows have all but melted but it was still a bit chilly, hovering around freezing and a brisk breeze blowing in off the ice. There’s birds everywhere, sandpipers, plovers, geese and redpolls. Snow buntings keep up a lovely chorus throughout the day. I’ve been busy meeting and catching up with colleagues at the North Slope Borough Department of Wildlife Management who support much of our work on beluga whales, polar bears and seals in the Arctic. I’ve had a little companion for a day or so sharing the ARF compound as I was the lone occupant for most of those first five days. Red foxes appear to be on the increase but it’s still rare to see them this far north….it doesn’t get any further north on the mainland of the US!
On Saturday, Robert Suydam, one of NSB DWM’s senior scientists, and I took a charter plane with 1,350 lbs of gear down to Point Lay and have been busy getting all the boats and motors set up, meeting with friends old and new. Late Monday evening we took one of the boats over to the old village site. There’s still some ice and quite a lot of wildlife including a little groups of terns and a numerous ground squirrels standing sentinel along the sew-ward coast looking out across the ice to the lowering sun. I collected some samples from bearded and ringed seals and plan to do more sampling over the coming days, both here and in Barrow before heading south to Anchorage and then west to the Aleutians."
Life Sciences South Florida
April 1, 2017
We are so proud!
On Saturday, Jorge presented at the Life Sciences South Florida conference and educated people on stock origins of Stellar Sea lions in Alaska: Chiswell Island Rookery.
Jorge placed second in oral presentations!!
Way to make us look good, Jorge!!
For a crash course on Stellar sea lions, watch this video from some of our collaborators as they conduct field work from a research vessel to the western Aleutian Islands.
Special thanks to Tom Gelatt and the Alaska Ecosystems Program at the National Marine Mammal Lab for allowing us to post their video. Check out their lab and current research here.
Ocean Science Lecture Series
February 22, 2017
Heidi and Jeremie presented at the Ocean Science Lecture Series tonight. Two auditoriums full of interested public members learned about our current research on immune function genes and the new technology we are using. The rave reviews after the presentation highlighted what a home run this was!
Florida Field Work
February 14, 2017
Nothing says romance like a day of field work!
Jeremie spent the day collecting water samples for an eDNA pilot study. Chocolates and flowers are overrated anyway.
North of the Wall
June 26, 2016
Dignity, Grace and Science...
August 21, 2015
Summer means field season for Arctic research; So, we shipped our fearless leader North of the Wall (do not fear, no GoT spoiler alerts are subliminally embedded in this post), with sampling kits and new protocols for our research. The climate situation and melting Arctic makes an already challenging environment even more unpredictable and volatile, so field work is not for the faint of heart nor creature of comfort! We will update the blog with more pics and information on the field season as the ravens come in. The rest of PBBE is holding down the fort in Westeros, wrapping up projects and finalizing reports.
Man, we could really use a dragon about now.
A little Friday humor to ease the sting of blank gels and empty tubes.
There, there, Doctor. It happens to the best of us!
Flash Back Friday
July, 2015
YouTube clip from eppaligy; Scene from YOUNG FRANKENSTEIN (1974)
In the middle of a very hot summer on the Treasure Coast,
we thought it appropriate to reminisce about a slightly (ha!) cooler day during January in Alaska. We had the best time meeting these lovable sled dogs and playing in the snow!
Greg is doing important field work in Alaska, as we speak (Hi Greg and friends!), to gather baseline data on beluga whales. He promised us to take lots of pictures and hopefully video footage of the remote basecamp site, so we can show a glimpse into the life of an Arctic field researcher!
Summer time!
July, 2015
For PBBE, summer time means it is All Systems GO in the lab! We have several projects firing on all cylinders right now, and Sarah, Tatiana, Heidi and Jorge are all milling about in the lab, running through an endless cycle of tips, dishes, tubes and agarose gels!
Here is Jorge, all suited up and getting trained by Sarah on aDNA techniques for one of their pilot projects.
It's the most wonderful time of the year...
December, 2014
PBBE finished the year with a BANG. We were waiting to hear the results from the final proposal we had out, and it was confirmed today that the full proposal for our major initiative was accepted and the grant was awarded! This project will push the boundaries of our immunogenetics and genomics research further than it's ever been; and in the process, we are making collaborations with top class scientists, forming new relationships with institutions, and bridging fields of research that seldomly overlap... and that is just one of the many proposals we got awarded (phew)!
2014 was one of the most successful years for us to date: We have several papers in various stages of submission, we've finished a few more projects that are now in the queue for reports and manuscripts, our tours, outreach and education was wildly popular and we have had an incredibly rewarding granting season (which means everyone will be making frequent blog appearances - with some new faces too)!
2015 is proving to be an incredibly busy and productive year already, but before we get too far ahead into next year, we wanted to take this time to say:
Happy Holidays from our family to yours
Check back with us frequently, as we have tons of exciting things kicking off in the Spring! See you guys in 2015!
We're taking this show on the road
November, 2014
Greg, Heidi and Tatiana each had abstacts accepted for posters at the Alaska Marine Science Symposium in Anchorage, Alaska this January! We will be presenting on beluga whales- updating everyone on the population genetic story and revealing some new MHC findings!
We will be sure to document our excursion here... two girls from Florida and one girl from New Mexico running around Alaska during January should make for some hilarious photos.
All in a days work
September, 2014
Shout out to the Big Cheese (Greg) for getting an awesome paper published in Molecular Ecology. To read about how resource limitation is affecting the distribution and genetic variation of Stellar sea lions in a dramatic and unusal way, head over to our publications page!
Greg's picture also made the cover... beauty and brains!
Bravo, sir!
Signed, sealed, delivered...
September 17, 2014
Today, HBOI, Mercyhurst University and OVIASC signed an MOU (Memorandum of Understanding). This formal agreement paves the way for artifacts found at the Old Vero Man site to be processed at HBOI's ancient DNA lab. PBBE gave media tours and answered questions about our ancient DNA work and some of the other exciting current projects we are working on. Check out our ancient DNA page for more info!
aDNA extraction
September 16, 2014
Have you ever wondered how we can extract DNA from hard materials, like bone or ivory? Or what kind of laboratory we need to extract ancient DNA?
WELLLLLL, then you are in the RIGHT place! We put together a quick video detailing the first few steps of DNA extraction from a Narwhal tooth (yeah... we think that's pretty cool too!)
Check us out being all legit and science-y:
the Data Ninja strikes again!
September 12, 2014
Heidi is making HUGE breakthroughs on her nextgen data, and as you can tell by Greg's shocked and happy face, it's ridiculously exciting!! (WTF media are always poised and ready to capture action shots of the PBBE team).
We took bets on how many alleles the data revealed (because who doesn't like a little bit of competition amongst collegues?!). Heidi kept us on the edge of our seats all weekend, and revealed in our Monday meeting that Sarah won...
But we are going to keep YOU on the edge of your seat. The number of alleles that Heidi has discovered in her game changing approach to next generation sequencing will have to remain a secret a little while longer until all analysis is finished. We will definitely be the first to tell you when her paper is in press!
Summertime, and the livin' is easy
July 22, 2014
We are baaaaack!
Actually, we never really left. Sorry for the long delay in posting, but we have been SUPER busy with exciting things. Brace yourselves for a lengthy post, but we need to get you all caught up:
the QuantStudio 12K FLEX has arrived!!
This baby will handle all (and more!) of our qPCR needs. We are adding an additional page to the website to detail all of the equipment, analysis capabilities and services we offer, so hang tight for that - we will include a link here when the page is live!
Once we had the platform in our grubby paws, we went through an extensive 2 day training on how to use the software and about the inner workings of the machine itself. Here are some pics of us nerding out during the training and driving the engineers crazy with 10 billion questions. We can't help it. We really like new toys.
All Things Considered...
We were super excited when we heard Sascha Cordner, from Florida Public Radio/WFSU-FM, wanted to talk to us about our research!
It was a great experience to sit down with Sascha and discuss our interesting findings on the dolphins in the Indian River Lagoon, what the results mean, and what the next steps are for our future research.
Click on the link to hear some audio gold from PBBE:
http://news.wfsu.org/post/how-dolphins-genetics-could-help-find-answers-mysterious-animal-die
We were so excited to hear ourselves on the radio - you probably thought we won a recording contract!
It's Official!!!
Credit Sascha Cordner / WFSU-FM
The best volunteer ever just became the best intern ever.
Jorge has made it to the big leagues! (humor us)
He is taking the lead on a really cool project, looking at immune genes in multiple species of cetaceans. This kind of broad survey of species, twinned with detailed analysis at specific immune response loci has never been done before - and his pilot project already yielded some intriguing data!
Part of congratulating him on his promotion involved going over to the -20C bunker and grabbing the samples he needed (it's the middle of summer and seriously, really cold in there!). Nobody ever said research was a glamorous gig.
Here's an official warm welcome to the PBBE family, Jorge!! We'll remember the parkas next time!
Extra Extra! Read all about it...
May 16, 2014
PBBE has made the big leagues!!
The research Sarah Rodgers completed for her master's thesis has caught the media's attention!
Sarah used genetic tools to fingerprint Indian River Lagoon and coastal Atlantic bottlenose dolphins, and uncovered new information on their population structure and dispersal. Her incredible findings shed light on what had been accepted dogma in the dolphin community for more than 40 years. Her results will have to be considered in any future experimental design and research projects!
To read more about Sarah's project, see the
Check out the newspaper article from TC Palm
And last but not least, if you are in the mood for some light reading, see Sarah's
We'll be sure to thank all the people who helped us make it to Hollywood.
This project would not have been possible without public funding from Harbor Branch specialty license plates and research collaborations with Hubbs-SeaWorld Reasearch Institute
Oh, hey there Friday...
March 21, 2014
You sexy thing, we missed you!
Another week logged in the trenches, another list of tasks crossed off!
Heidi had a breakthrough on her data (I don't want to give all the secrets away.. but we were doing the happy dance with her!!)
Sarah updated our inventory and cost spreadsheets with the new prices released from retailers. (It sounds like no big deal, but trust us, it's tedious work!)
Tat hung out with Jorge and supervised his next set of extractions and helped him with his trouble samples for PCR. She's also working on her manuscript... stay tuned for that- Should be submitted sooner rather than later (fingers crossed)!
And Greg has been in more meetings than any person should be subjected to. Honestly. He's probably close to hitting some kind of record.
All in all, it's been a crazy week (rumor has it that pigs were spotted flying around the Branch), and we haven't been this excited about a Friday since... well... last Friday.
Happy Spring. We hope you get outside and enjoy the sunshine!
Adios, amiga!
March 19, 2014
Today, was a bittersweet day.
We said goodbye to our friend and co-worker, Liz.
While we are happy for her, and know that she is moving on to bigger and better things, we will miss her (and her ridiculously delicious pumpkin bread) terribly!
In true PBBE fashion, we bid her adieu with slightly offensive cupcakes. (In case you're wondering, they taste better than PC cupcakes!)
Good luck on your next adventure, Liz! And remember, don't let the muggles get you down!
There can be only thumb...
March 12, 2014
Ever wonder how scientists settle their differences?
Well, we can't speak for other labs, but we prefer to settle any major decisions, discussions, or differences over a good old fashioned game of thumb wrestling.
However- we didn't take into account how freakishly strong Dr. Hemmings thumbs are....
Old Vero Man: 1
PBBE: 0
We are currenlty adjusting our work out regimen. Obviously, pipette calisthenics are no match for archaeologists.
Bands or Bust!!
March 7, 2014
Another Friday success story for the books!
Jorge is leading a pilot study on identifying unknown cetacean samples using mitochondrial DNA sequencing. In this picture, Jorge is holding up the image from his gel electrophoresis. He was checking to see if his first solo attempt at PCR reaction was succesful... and it was! Bands fluoresced at the proper length, and there was no contamination!!
Our little volunteer is growing up so quick!
Ladies and gentlemen, THIS is what being on the edge of cutting research looks like.
Dr. Pagan is this close to making a breakthrough on her next generation sequencing data!!! If everything goes according to plan, the lab techniques Tatiana used over the last two years for her thesis will be considered a thing of the past. (Don't worry, they won't be able to get rid of the lab gangster that easily!)
We'll be sure to keep you posted on Heidi's exciting work. It involves cool buzzwords like: phase genotypes, promoter regions and MHC. Also, she needs at least two computers and several monitors to run her data pipeline, so you know she's legit.
The Data Ninja
March 6, 2014
When we are extracting and sequencing samples, days in the lab can be pretty long. Since you are isolated to reduce the risk of contamination, working on ancient DNA can also get a little lonely.
What do you do when you are trapped in a little room by yourself, dressed in a space suit, with only old bones to keep you company?
You dance.
Sometimes, you just have to dance.
The Microsat Master
March 6, 2014
That smile can mean only one thing: thermal cyclers are buzzing!
Sarah is in the throws of optimizing microsatellite primers for her samples. There is no master mix combination that will go untried and no limits to the color coordination that will take place. Do not underestimate the power of color coordinating in the lab! Between color of tubes, color of trays, and color of pens to write notes about said tubes in the lab book- the combinations are almost limitless.
If you don't get ridiculously excited about office supplies, this might not be the lab for you.